RetrogeneDB ID: retro_sita_33

Retrocopy location

• Organism: Foxtail millet (Setaria italica)
• Coordinates: 6:27132973..27133936(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Si014102m.g
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Si030120m.g
• Aliases: None
• Description: None

Sequence

>retro_sita_33
ATGGCGAGCCTGACGGTGCCGCCGGTGCCTACGTGGCCCCGGCAGGACGCCATCGACCTCCACAGGGCGTTCAAAGGTTT
CGGCTGCGACAGCACGACGGTGATCAACATCCTCGCCCACCGCGACGCGGCGCAGCGCGCGCTGATCCAGCAGGAGTACC
GCGCCGTGTTCAACCAGGACCTCGCCCGCCGCATCGCCTCCGAGCTCAGCGGCCACCACAAGCGCGCCATGCTGCTGTGG
CTCCTGGACCCGGCCTCCCGCGACGCCACCATCCTGAAGCAGGCCCTCACCGGTGACGTCACCGACCTCCGCGCCGCCAC
GGAGGTGGTCTGCTCCCGAACCCCCTCGCAGCTCCAGATCATCCGGCACACCTACCGCGCCCGGTTCGGCTGCTACGTCG
AGCACGACGTCACCGAGCGGACCTCCGGCGACCACCAGCGGCTGCTGCTGGCGTACCTGGCGATCCCGCGCGCGGAGGGG
GCGGCGGCGGTGGACCCGTCGCTGGCGGCGCTGGACGCCCGGGAGCTCTTCAAGGCCGGGGAGCGGCGGCTGGGCACCGA
CGAGCGCGCCTTCATCCGGGTGTTCAGCGAGCGGAGCTGGGCGCACCTGGCGGCGGTGGCGCGGGCGTACCACCACATGT
ACGACCGGTCGCTGGAGCAGGCGGTGAAGGGCGAGACGTCGGGGAACTTCGGGTTCGGCCTCCTCACCGTGCTCCGGTGC
GCCGCCGACAGCCCGGCGAGGTACTTCGCCAAGGTGCTCCACAAGGCGATGAAGGGGCTTGGCACCAGCGACTCGGCGCT
GATCCGGGTGGTGGTGACGCGGGCGGAGGTGGACATGCAGTACATCAAGGCCGAGTACCACAGGATGTACAAGCGCTCCC
TCCCCGACGCCATCCACTCCGAGACGTCCGGCAACTACCGCACCTTCCTCCTCTCCCTTGTCGGACGCGACAGGACCTAC
TGA

Alignment

ORF - retro_sita_33 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.79 %
• Parental protein coverage: 80.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASLTLPPAPPNPRQDAIDLHKAFKGFGCDSTAVINILTHRDSVQRGLIQQEYRAMYHEELSQRISSELS
          MASLT.PP.P..PRQDAIDLH.AFKGFGCDST.VINIL.HRD..QR.LIQQEYRA.....L..RI.SELS
Retrocopy MASLTVPPVPTWPRQDAIDLHRAFKGFGCDSTTVINILAHRDAAQRALIQQEYRAVFNQDLARRIASELS

Parental  GNHKKAMLLWILDPAGRDATVLREALSGDTMDLRAATEIICSRTPSQLQIMKQTYFARFGTYLEHDIGHH
          G.HK.AMLLW.LDPA.RDAT.L..AL.GD..DLRAATE..CSRTPSQLQI...TY.ARFG.Y.EHD....
Retrocopy GHHKRAMLLWLLDPASRDATILKQALTGDVTDLRAATEVVCSRTPSQLQIIRHTYRARFGCYVEHDVTER

Parental  TSGDHQKILLAYMGIPRYEG-PEVDPTIVTHDAKDLYKAGEKRLGTDEKTFIRIFTERSWAHIASVSSAY
          TSGDHQ..LLAY..IPR.EG...VDP.....DA..L.KAGE.RLGTDE..FIR.F.ERSWAH.A.V..AY
Retrocopy TSGDHQRLLLAYLAIPRAEGAAAVDPSLAALDARELFKAGERRLGTDERAFIRVFSERSWAHLAAVARAY

Parental  HHMYDRKLEKVIKSETSGNFAFALLTILRC-AESPAKYFAKLLRKAMKGLGTDDKTLIRVVVTRTEIDMQ
          HHMYDR.LE...K.ETSGNF.F.LLT.LRC.A.SPA.YFAK.L.KAMKGLGT.D..LIRVVVTR.E.DMQ
Retrocopy HHMYDRSLEQAVKGETSGNFGFGLLTVLRCAADSPARYFAKVLHKAMKGLGTSDSALIRVVVTRAEVDMQ

Parental  YIKAEYFKKYKKPLGEAINSETSGHYRTFLLSLVG
          YIKAEY...YK..L..AI.SETSG.YRTFLLSLVG
Retrocopy YIKAEYHRMYKRSLPDAIHSETSGNYRTFLLSLVG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Setaria italica was not studied using RNA-Seq expression data.

ChIP-Seq

Setaria italica was not studied using ChIP-Seq data.

EST

Setaria italica was not studied using EST data.

TSS

Setaria italica was not studied using FANTOM5 data.

Lab

retro_sita_33 was not experimentally validated.

Homology

Retrocopy orthology:

Setaria italica does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Zea mays	GRMZM2G009136	1 retrocopy	retro_zmay_25,
Sorghum bicolor	Sb02g024090	1 retrocopy	retro_sbic_6,
Setaria italica	Si030120m.g	1 retrocopy	retro_sita_33 ,